crossing96/oncoscreening huggingface dataset:
Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data.	Tumors are made of evolving and heterogeneous populations of cells which arise from successive appearance and expansion of subclonal populations, following acquisition of mutations conferring them a selective advantage. Those subclonal populations can be sensitive or resistant to different treatments, and provide information about tumor aetiology and future evolution. Hence, it is important to be able to assess the level of heterogeneity of tumors with high reliability for clinical applications. In the past few years, a large number of methods have been proposed to estimate intra-tumor heterogeneity from whole exome sequencing (WES) data, but the accuracy and robustness of these methods on real data remains elusive. Here we systematically apply and compare 6 computational methods to estimate tumor heterogeneity on 1,697 WES samples from the cancer genome atlas (TCGA) covering 3 cancer types (breast invasive carcinoma, bladder urothelial carcinoma, and head and neck squamous cell carcinoma), and two distinct input mutation sets. We observe significant differences between the estimates produced by different methods, and identify several likely confounding factors in heterogeneity assessment for the different methods. We further show that the prognostic value of tumor heterogeneity for survival prediction is limited in those datasets, and find no evidence that it improves over prognosis based on other clinical variables. In conclusion, heterogeneity inference from WES data on a single sample, and its use in cancer prognosis, should be considered with caution. Other approaches to assess intra-tumoral heterogeneity such as those based on multiple samples may be preferable for clinical applications.	bladder
Incidence and prognosis of clinically significant incidental prostate cancer after radical cystectomy for bladder cancer.	OBJECTIVE: To evaluate the prevalence and significance of incidental prostate cancer in patients after radical cystectomy for bladder cancer, as well as its impact in terms of overall survival and biochemical recurrence. METHODS: Patients with bladder cancer treated with radical cystectomy in our hospital between 1998 and 2014 were included in the study. None of the patients had previous history of prostatic adenocarcinoma. Complete embedding of the prostate gland as whole mount serial section of the radical cystectomy specimens was done. RESULTS: 180 patients were included. The mean age was 69.71 years with a median follow-up of 34.2 months. Three groups were analyzed: non-incidental prostate cancer (n=136), non-significant incidental prostate cancer (n=28) and significant incidental prostate cancer (n=16). During follow-up, 50 patients (27.78%) died from bladder cancer. There were no differences in overall survival between patients with or without prostate cancer, neither between patients with significant nor insignificant prostate cancer in the radical cystectomy specimens. Biochemical recurrence was not observed in any patient. CONCLUSIONS: Incidental prostate cancer had a higher prevalence than previously expected in our cohort (24.4%), but it had no impact in overall survival of patients not even in those with a significant prostate cancer. No biochemical recurrence was reported during the study.	bladder
7-Chloroquinoline-1,2,3-triazoyl carboxamides induce cell cycle arrest and apoptosis in human bladder carcinoma cells.	In the present study, the antitumoral properties of a series of 7-chloroquinoline-1,2,3-triazoyl-carboxamides (QTCA) were investigated by analyzing their cytotoxic activities against human bladder cells (5637; grade II carcinoma). In addition, their effects on cell viability, cell cycle arrest mechanisms, apoptosis induction, in silico molecular docking, and detection of pro-apoptotic and anti-apoptotic proteins were evaluated. The cytotoxicity assay identified major dose- and time-dependent cytotoxic effects in 5637 cells after they were exposed to treatment with QTCA, only minimal effects were observed on normal cells. A live/dead assay confirmed that significant cell death, arrest in the G0/G1 phase and apoptosis were associated with treatment by 1-(7-Chloroquinolin-4-yl)-5-methyl-N-phenyl-1H-1,2,3-triazole-4-carboxamide (QTCA-1) and 1-(7-Chloroquinolin-4-yl)-N-(4-fluorophenyl)-5-methyl-1H-1,2,3-triazole-4-carboxamide (QTCA-4). The in silico results indicated that these compounds acted through different mechanisms for the induction of cell cycle arrest and apoptosis. Western blotting confirmed the binding of the QTCAs to pro- and anti-apoptotic proteins. In conclusion, QTCA-1 and QTCA-4 are promising candidates for inducing cytotoxicity, cell cycle arrest, and apoptosis in human bladder cancer cells.	bladder
Effect of a patient education and rehabilitation program on anxiety, depression and quality of life in muscle invasive bladder cancer patients treated with adjuvant chemotherapy.	This study aimed to investigate the effect of a patient education and rehabilitation program (PERP) on anxiety, depression, and quality of life in muscle invasive bladder cancer (MIBC) patients underwent adjuvant chemotherapy.One hundred and thirty MIBC patients about to receive adjuvant chemotherapy with 4-cycle gemcitabine and cisplatin (GC) regimen (16 weeks) were consecutively enrolled and randomly allocated into PERP group and control group as 1:1 ratio. Hospital Anxiety and Depression Scale (HADS) anxiety and depression scores and Quality of Life Questionnaire (QLQ-C30) scores were assessed before treatment (W0) and after treatment (W16).After 16-week treatment, PERP group exhibited decreased HADS anxiety score (P = .036), ΔHADS anxiety score (W16-W0) (P < .001) and percentage of anxiety patients (P = .019) compared to control group. And PERP group presented with numerically reduced HADS depression score but without statistical significance (P = .076) compared to control group, while lower ΔHADS depression score (W16-W0) (P = .014) and percentage of depression patients (P = .015) compared to control group. As to quality of life, QLQ-C30 global health status score (P = .032), Δglobal health status score (W16-W0) (P = .003) and Δfunctional score (W16-W0) (P = .005) were higher in PERP group compared to control group. However, no difference of QLQ-C30 functional score (P = .103), QLQ-C30 symptom score (P = .808) or Δsymptom score (W16-W0) (P = .680) was observed between two groups.PERP relieves anxiety, depression and improves quality of life in MIBC patients underwent adjuvant chemotherapy.	bladder
SP600125 enhances C-2-induced cell death by the switch from autophagy to apoptosis in bladder cancer cells.	BACKGROUND: A natural compound Jaspine B and its derivative possess potential anti-cancer activities; However, little is known about the underlying mechanism. Here, the role of a new autophagy inducer Jaspine B derivative C-2 in suppressing bladder cancer cells was researched in vitro and in vivo. METHODS: The underlying mechanisms and anticancer effect of C-2 in bladder cancer cells were investigated by MTT, western blotting, immunoprecipitation and immunofluorescence assays. The key signaling components were investigated by using pharmacological inhibitors or specific siRNAs. In vivo, we designed a C-2 and SP600125 combination experiment to verify the effectiveness of compound. RESULTS: C-2 exhibits cytotoxic effect on bladder cancer cells, and JNK activated by C-2 triggers autophagy and up-regulates SQSTM1/p62 proteins, contributing to activation of Nrf2 pathway. Utilization of JNK inhibitor SP600125 or knockdown of JNK by siRNA potentiate the cytotoxicity of C-2 through down-regulation of p62 and LC3II proteins and up-regulation of active-Caspase3 proteins, enhance the cell death effect, facilitating the switch from autophagy to apoptosis. In vivo study, C-2 suppresses tumor growth in a xenograft mouse model of EJ cells without observed toxicity. Combined treatment with SP600125 further enhances tumor inhibition of C-2 associated with enhanced activation of caspase3 and reduction of autophagy. CONCLUSIONS: It reveals a series of molecular mechanisms about SP600125 potentiate the cytotoxicity and tumor inhibition of C-2 in bladder cancer cells through promoting C-2-induced apoptosis, expecting it provides research basis and theoretical support for new drugs development.	bladder
Bladder cancer and its mimics: a sonographic pictorial review with CT/MR and histologic correlation.	Bladder cancer is the most common cancer of the urinary system and often presents with hematuria. Despite its relatively high incidence, bladder cancer is often under-recognized sonographically. Moreover, even when bladder abnormalities are identified, numerous other entities may mimic the appearance of bladder cancer. Given the incidence and prevalence of bladder cancer, it is important to recognize its variable appearance sonographically and distinguish it from its common mimics. We review the sonographic appearance of bladder cancer and its mimics, providing correlative CT/MR imaging as well as pathology. We stress the importance and advantage of ultrasound as a dynamic imaging modality, with the ability to optimize distinguishing bladder cancer from similar-appearing entities.	bladder
Screening logs from a pilot randomized controlled trial of radical cystectomy versus chemoradiation therapy for muscle-invasive bladder cancer.	INTRODUCTION AND OBJECTIVES: There is growing interest in a bladder preservation approach using chemoradiation therapy with transurethral resection of bladder tumor (TURBT), i.e., combined modality treatment (CMT), for muscle-invasive bladder cancer (MIBC). We have initiated a pilot study to determine feasibility of conducting a larger-scale clinical trial comparing CMT to radical cystectomy (RC) in patients with MIBC. Here we present the screening logs from the recruitment phase of this trial. METHODS: Patients who were diagnosed to have MIBC after TURBT between April 2016 and August 2017 and considered to be candidates for surgery were enrolled in this prospective, single center, randomized controlled pilot feasibility trial and scheduled to undergo RC (with neoadjuvant chemotherapy if appropriate) or CMT. RESULTS: Of 62 patients screened during the recruitment phase, only 5 were found to be suitable candidates for either treatment modality hence eligible for randomization. The reasons for exclusion were as follows: multifocal disease (n = 24, 40%), variant histology (n = 15, 25%), previous pelvic radiation (n = 6, 10%), severe lower urinary tract symptoms (n = 5, 8.3%), unwillingness to be enrolled (n = 8, 13.3%), and receipt of neoadjuvant chemotherapy (n = 2, 3.3%). One of the 5 eligible patients was randomized to CMT but was subsequently switched to RC because of a high tumor burden, 1 was randomized to RC, 2 were randomized to CMT but subsequently underwent TURBT and were considered ineligible because of extensive bladder disease, and 1 elected to undergo RC. CONCLUSIONS: We identified many patients with MIBC over a period of 16 months. However, the number of patients eligible to receive chemotherapy and in whom cystectomy and radiation therapy were both valid options was not as high as previously reported in retrospective CMT series. Many patients were excluded after TURBT. Our preliminary data indicate that only a very small subset of patients with MIBC are ideal candidates for CMT. Further research is required to identify patients who are suitable for CMT.	bladder
Eligibility and Radiologic Assessment in Adjuvant Clinical Trials in Bladder Cancer.	OBJECTIVE: To harmonize eligibility criteria and radiographic disease assessments in clinical trials of adjuvant therapy for muscle-invasive bladder cancer (MIBC). METHODS: National experts in bladder cancer clinical trial research, including medical and urologic oncologists, radiologists, biostatisticians, and patient advocates, convened at a public workshop on November 28, 2017, to discuss eligibility, radiographic entry criteria, and assessment of disease recurrence in adjuvant clinical trials in patients with MIBC. RESULTS: The key workshop conclusions for adjuvant MIBC clinical trials included the following points: (1) patients with urothelial carcinoma with divergent histologic differentiation should be allowed to enroll; (2) neoadjuvant chemotherapy is defined as at least 3 cycles of neoadjuvant cisplatin-based combination chemotherapy; (3) patients with muscle-invasive, upper-tract urothelial carcinoma should be included in adjuvant trials of MIBC; (4) patients with severe renal insufficiency can enroll into trials using agents that are not renally excreted; (5) patients with microscopic surgical margins can be included; (6) patients should undergo a standard bilateral lymph node dissection prior to enrollment; (7) computed tomographic (CT) imaging should be performed within 4 weeks prior to enrollment. For patients with renal insufficiency who cannot undergo CT imaging with contrast, noncontrast chest CT and magnetic resonance imaging of the abdomen and pelvis with gadolinium should be done; (8) biopsy of indeterminate lesions to evaluate for malignant disease should be done when feasible; (9) a uniform approach to evaluate indeterminate radiographic lesions when biopsy is not feasible should be included in any trial design; (10) a uniform approach to determining the date of recurrence is important in interpreting adjuvant trial results; and (11) new high-grade, upper-tract primary tumors and new MIBC tumors should be considered recurrence events. CONCLUSIONS AND RELEVANCE: A uniform approach to eligibility criteria, definitions of no evidence of disease, and definitions of disease recurrence may lead to more consistent interpretations of adjuvant trial results in MIBC.	bladder
Does asymptomatic bacteriuria affect the response to intravesical bacillus Calmette-Guérin?	OBJECTIVE: To determine the initial response to intravesical bacillus Calmette-Guérin and the 3-year recurrence rate of high-risk non-muscle-invasive bladder cancer in patients who have asymptomatic bacteriuria. METHODS: Response and recurrence rates were investigated in 505 patients with high-risk non-muscle-invasive bladder cancer after treatment with induction bacillus Calmette-Guérin (TICE strain) therapy. Initial response was determined after 3 months and patients were followed every 3-6 months for 3 years. Before bacillus Calmette-Guérin and each follow-up cystoscopy, urine cultures were obtained, stratified as no growth, <104, >104 or >105 colony-forming unit/mL. Any degree of bacteriuria on culture was classified as asymptomatic bacteriuria. RESULTS: Of the 505 cases, 270 (53%) had asymptomatic bacteriuria. A total of 89% of patients with asymptomatic bacteriuria showed a complete response to bacillus Calmette-Guérin versus 76% of uninfected patients (P = 0.001), and 75% of bacteriuric patients survived tumor-free for 3 years versus 65% of uninfected patients. CONCLUSIONS: Chronic bacteriuria might enhance the response of high-risk non-muscle-invasive bladder cancer to intravesical bacillus Calmette-Guérin and result in longer tumor-free survival than uninfected patients.	bladder
Retrospective study of systemic immune-inflammation index in muscle invasive bladder cancer: initial results of single centre.	"PURPOSES: We aimed to evaluate the prognostic value of the preoperative systemic immune-inflammation index (SII) in patients who underwent radical cystectomy due to muscle invasive bladder cancer (MIBC). METHODS: We researched our cystectomy database between April 2006 and December 2018. Demographic data, operation and postoperative data were recorded. There were 191 MIBC patients who underwent radical cystectomy. After detailed analyses, preoperative SII was calculated by the formula as ""(neutrophil) × (platelet)/(lymphocyte)"". Cancer-specific survival (CSS) and overall survival (OS) were examined. The prognostic value of SII was analysed with univariate and multivariate Cox proportional hazards regression models. Receiver operating characteristic (ROC) was used to determine the optimum SII. Significant P was P < 0.05. RESULTS: The mean follow-up was 37 ± 6.7 months. The mean age of patients was 62.1 ± 9 years. The optimal cutoff value of SII was determined as 843 in ROC curve (area under the curve: 0.9; P < 0.001). The CSS and OS were significantly poor in patients with higher SII level (respectively; P < 0.001, P = 0.04). Gender, lymph node involvement, pathologic stage, grade and SII were statistically significant in multivariate Cox proportional hazards regression model for CSS. CONCLUSIONS: Preoperative elevated SII could be an independent prognostic factor in MIBC patients who underwent radical cystectomy. If SII > 843, CSS might be poor. Our results should be confirmed with randomised-controlled prospectively designed future studies with large cohorts."	bladder
Toward Automated In Vivo Bladder Tumor Stratification Using Confocal Laser Endomicroscopy.	Purpose: Urothelial carcinoma of the bladder (UCB) is the most common urinary cancer. White-light cystoscopy (WLC) forms the corner stone for the diagnosis of UCB. However, histopathological assessment is required for adjuvant treatment selection. Probe-based confocal laser endomicroscopy (pCLE) enables visualization of the microarchitecture of bladder lesions during WLC, which allows for real-time tissue differentiation and grading of UCB. To improve the diagnostic process of UCB, computer-aided classification of pCLE videos of in vivo bladder lesions were evaluated in this study. Materials and Methods: We implemented preprocessing methods to optimize contrast and to reduce striping artifacts in each individual pCLE frame. Subsequently, a semiautomatic frame selection was performed. The selected frames were used to train a feature extractor based on pretrained ImageNet networks. A recurrent neural network, in specific long short-term memory (LSTM), was used to predict the grade of bladder lesions. Differentiation of lesions was performed at two levels, namely (i) healthy and benign vs malignant tissue and (ii) low-grade vs high-grade papillary UCB. A total of 53 patients with 72 lesions were included in this study, resulting in ∼140,000 pCLE frames. Results: The semiautomated frame selection reduced the number of frames to ∼66,500 informative frames. The accuracy for differentiation of (i) healthy and benign vs malignant urothelium was 79% and (ii) high-grade and low-grade papillary UCB was 82%. Conclusions: A feature extractor in combination with LSTM results in proper stratification of pCLE videos of in vivo bladder lesions.	bladder
Development and validation of a prognostic nomogram for patients with intravesical recurrence after radical nephroureterectomy for non-metastatic upper tract urothelial carcinoma.	PURPOSE: To develop and validate a prognostic nomogram for patients with intravesical recurrence (IVR) after radical nephroureterectomy (RNU) for non-metastatic upper tract urothelial carcinoma (UTUC). METHODS: The clinical data of 468 patients registered in the surveillance, epidemiology and end results database between 2010 and 2015 were retrospectively analyzed. Multivariate analysis using the Cox proportional hazard model was used to determine independent prognostic factors for the development of a nomogram to predict the 1-, 3-, and 5-year probability of individual cancer-specific survival (CSS). Moreover, the nomogram was internally validated using receiver operating characteristic curves and calibration plots. RESULTS: Age at IVR > 80 years, UTUC stage ≥ T3, bladder cancer (BC) stage T1, and muscle-invasive BC (stage ≥ T2) were identified as independent risk factors for CSS in patients with IVR after RNU, whereas a time interval of > 24 months between UTUC and BC was an independent protective factor. The 1-, 3-, and 5-year predictive accuracies of our nomogram were 0.74, 0.70, and 0.71, respectively. Additionally, 1-, 3-, and 5-year calibration curves demonstrated perfect agreement between the nomogram-predicted and the actual CSS. CONCLUSIONS: This study developed and internally validated the first nomogram to date to predict individual prognosis in patients with IVR after RUN for UTUC. This nomogram can be used for patient counseling and for designing clinical trials.	bladder
Ureteroenteric strictures: a single center experience comparing Bricker versus Wallace ureteroileal anastomosis in patients after urinary diversion for bladder cancer.	BACKGROUND: To evaluate the outcome and complication rate in a single institution experience using the two most commonly used techniques of ureteroenteric anastomosis, the Bricker and Wallace anastomosis. METHODS: A total of 137 patients underwent ileal conduit for bladder cancer. Ureters were anastomosed by two experienced surgeons, one performing a Bricker and the other, a Wallace anastomosis. Stricture was identified during clinical follow-up. RESULTS: Seventy-five patients underwent a Bricker anastomotic, and 65 received a Wallace anastomosis. The average age was 70 in both groups, males were predominant (66% Bricker, 70% Wallace). Follow up period was 36.5 months in Bricker group and 17 months in Wallace group. In both groups, the body mass index (BMI) was similar (26.1 kg/m(2) Bricker and 26.4 kg/m(2) Wallace). We observed that the stricture rate after performing the Bricker anastomosis technique was 25.3% (19/75) as compared to 7.7% (5/65) after Wallace anastomosis technique, which was statistically significant (p = 0.001). In the Bricker group, patients with strictures had higher BMI (28.3 vs. 25.7 kg/m(2), p = 0.05). On average it took 8.5 months in the Bricker group and three months in the Wallace group (p = 0.6) to develop stricture. CONCLUSIONS: The stricture rate was significantly higher when Bricker technique was applied. Although the BMI was not different in both groups, patients with a higher BMI were more likely to develop stricture. We believe that the approach of the separate and refluxing technique of Bricker anastomosis especially in obese patients poses a higher risk for anastomotic stricture formation.	bladder
LncRNA-MALAT1 mediates cisplatin resistance via miR-101-3p/VEGF-C pathway in bladder cancer.	Cisplatin (CDDP)-based chemotherapy is a standard strategy for the clinical treatment of patients with bladder cancer (BC). However, the anti-tumor efficacy of cisplatin is affected by multiple chemoresistance with complex molecular mechanisms. Recent evidence highlights the crucial regulatory roles of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in the progression of cancers and development of drug resistance. However, the roles and underlying molecular mechanisms of MALAT1 in cisplatin resistance of the BC cells remain largely unclear. In this study, we firstly demonstrated that MALAT1 expression was up-regulated in the BC tissues compared to the normal adjacent tissues and elevated in the cancer cells compared to the epithelial immortalized cells. Secondly, we found that suppression of MALAT1 enhanced the chemotherapeutic drug sensitivity and inhibited the cisplatin resistance of the BC cells. Thirdly, we showed that MALAT1 affected the cisplatin resistance of the BC cells via regulating the miR-101-3p/VEGF-C pathway. In summary, this study demonstrates that MALAT1, miR-101-3p and VEGF-C form a regulatory axis to affect the chemo-resistance of BC cells to CDDP, and provides novel potential targets for treatment of BC.	bladder